首页|Long-read genome assemblies reveal a cis-regulatory landscape associated with phenotypic divergence in two sister Siniperca fish species
Long-read genome assemblies reveal a cis-regulatory landscape associated with phenotypic divergence in two sister Siniperca fish species
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Due to the difficulty in accurately identifying structural variants(SVs)across genomes,their impact on cis-regulatory divergence of closely related species,especially fish,remains to be explored.Recently identified broad H3K4me3 domains are essential for the regulation of genes involved in several biologica-processes.However,the role of broad H3K4me3 domains in phenotypic divergence remains poorly understood.Siniperca chuatsi and S.scherzeri are closely related but divergent in severa-phenotypic traits,making them an ideal model to study cis-regulatory evo-ution in sister species.Here,we generated chromosome-leve-genomes of S.chuatsi and S.scherzeri,with assembled genome sizes of 716.35 and 740.54 Mb,respectively.The evo-utionary histories of S.chuatsi and S.scherzeri were studied by inferring dynamic changes in ancestra-population sizes.To explore the genetic basis of adaptation in S.chuatsi and S.scherzeri,we performed gene family expansion and contraction analysis and identified positively se-ected genes(PSGs).To investigate the role of SVs in cis-regulatory divergence of closely re-ated fish species,we identified high-quality SVs as well as divergent H3K27ac and H3K4me3 domains in the genomes of S.chuatsi and S.scherzeri.Integrated analysis revealed that cis-regulatory divergence caused by SVs played an essential role in phenotypic divergence between S.chuatsi and S.scherzeri.Additionally,divergent broad H3K4me3 domains were mostly associated with cancer-related genes in S.chuatsi and S.scherzeri and contributed to their phenotypic divergence.
State Key Laboratory for Biocontrol,School of Marine Sciences,Sun Yat-sen University,Zhuhai,Guangdong 519000,China
China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology,Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai),Zhuhai,Guangdong 519000,China
Chinese Institute for Brain Research,Beijing 102206,China
Guangdong Province Key Laboratory for Aquatic Economic Animals,School of Life Sciences,Sun Yat-sen University,Guangzhou,Guangdong 510275,China
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National Natural Science Foundation of ChinaGuangdong Basic and Applied Basic Research FoundationKey-Area Research and Development Program of Guangdong ProvinceSeed Industry Development Project of Agricultural and Rural Department of Guangdong Province(2022)Innovation Group Project of Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)
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